Eigen gene/module correlation

Does + Eigen gene mean + overal module gene expression?

library(tidyverse)

── Attaching packages ────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.1       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.4.0  
✔ readr   1.3.1       ✔ forcats 0.4.0  
package ‘ggplot2’ was built under R version 3.5.2package ‘tibble’ was built under R version 3.5.2package ‘tidyr’ was built under R version 3.5.2package ‘purrr’ was built under R version 3.5.2package ‘dplyr’ was built under R version 3.5.2package ‘stringr’ was built under R version 3.5.2package ‘forcats’ was built under R version 3.5.2── Conflicts ───────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

library(WGCNA)

package ‘WGCNA’ was built under R version 3.5.2Loading required package: dynamicTreeCut
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:

    hclust



Attaching package: ‘WGCNA’

The following object is masked from ‘package:stats’:

    cor

load("../output/WGCNA_UN_all.Rdata")

expr <- expr.data.UN.t %>% 
  scale() %>%
  t() %>%
  as.tibble() %>%
  mutate(color=merge$colors,
         ID=colnames(expr.data.UN.t)) %>%
  select(ID, color, everything())

`as.tibble()` is deprecated, use `as_tibble()` (but mind the new semantics).
This warning is displayed once per session.

expr[1:10, 1:10]

expr_MEs <- MEs %>% 
  scale() %>% 
  t()  %>% 
  as.data.frame() %>% 
  rownames_to_column("ID") %>% 
  mutate(color=str_sub(ID, 3)) %>%
  select(ID, color, everything()) %>%
  bind_rows(., expr) %>%
  mutate(type=ifelse(str_detect(ID, "^ME"), "eigen", "gene")) %>%
  select(ID, color, type, everything())
expr_MEs

map(unique(expr_MEs$color), function(x) {
  expr_MEs %>%
    filter(color==x) %>%
    gather(key = "RIL", value="expression", -ID, -color, -type) %>%
    ggplot(aes(x=RIL, y=expression, group=ID, alpha=type, color=type )) +
    geom_line() +
    scale_alpha_manual(values = c("eigen" = 1, "gene" = 0.05)) +
    scale_color_manual(values = c("eigen" = "red", "gene" = "black")) +
    ggtitle(color)
})

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